nf-core/mhcquant issues and pull requests

#304 - Merging template updates

Pull Request - State: closed - Opened by jonasscheid 10 months ago - 2 comments

#303 - Important! Template update for nf-core/tools v2.12

Pull Request - State: closed - Opened by nf-core-bot 10 months ago

#302 - Fix docker container permissions for ms2rescore

Pull Request - State: open - Opened by jonasscheid 10 months ago - 2 comments

#301 - mzml renaming and fixed ion parameters

Pull Request - State: closed - Opened by steffenlem 11 months ago - 1 comment

#300 - Merge template updates

Pull Request - State: closed - Opened by jonasscheid 11 months ago - 1 comment

#299 - Fix decoydatabase creation

Pull Request - State: closed - Opened by jonasscheid 11 months ago - 1 comment

#298 - Test multiple variable and fixed modifications

Pull Request - State: closed - Opened by jonasscheid 11 months ago - 1 comment

#297 - Expose deeplc calibration set size param

Pull Request - State: closed - Opened by jonasscheid 11 months ago - 1 comment

#296 - Port local OpenMS modules to nf-core modules

Issue - State: open - Opened by jonasscheid 11 months ago
Labels: enhancement, help wanted

#295 - Important! Template update for nf-core/tools v2.11

Pull Request - State: closed - Opened by nf-core-bot 11 months ago

#294 - DEEPLC and MS2PIP doesnt work with multiple variable modifications

Issue - State: open - Opened by yannic-chen 11 months ago - 5 comments
Labels: bug

#293 - Add ms2rescore module, remove ms2pip and deeplc modules

Pull Request - State: closed - Opened by jonasscheid 12 months ago - 3 comments
Labels: enhancement

#292 - Alter the tsv outcome of quantified data

Pull Request - State: closed - Opened by marissaDubbelaar about 1 year ago - 1 comment

#291 - Alter tsv outcome

Issue - State: open - Opened by marissaDubbelaar about 1 year ago
Labels: enhancement, suggestion next release

#290 - Better multiQC report

Issue - State: open - Opened by marissaDubbelaar about 1 year ago
Labels: enhancement, suggestion next release

#289 - Re-itterate over the contributors

Issue - State: closed - Opened by marissaDubbelaar about 1 year ago
Labels: enhancement, suggestion next release

#288 - Replace DeepLC and MS2PIP wrappers with MS2Rescore

Issue - State: open - Opened by jonasscheid about 1 year ago
Labels: enhancement, suggestion next release

#287 - Create only one decoy database if no vcf_sheet is given

Issue - State: open - Opened by jonasscheid about 1 year ago
Labels: enhancement

#286 - Remove writing out all peaks when using Ion Annotator

Issue - State: open - Opened by jonasscheid about 1 year ago
Labels: enhancement, suggestion next release

#285 - Final changes for release 2.5.0

Pull Request - State: closed - Opened by jonasscheid about 1 year ago - 1 comment

#284 - Release 2.5.0

Pull Request - State: closed - Opened by jonasscheid about 1 year ago - 3 comments

#282 - Important! Template update for nf-core/tools v2.10

Pull Request - State: closed - Opened by nf-core-bot about 1 year ago

#281 - Support compressed input

Issue - State: open - Opened by jonasscheid about 1 year ago
Labels: enhancement, suggestion next release

#280 - Rearrange quant and prepare for release 2.5.0

Pull Request - State: closed - Opened by jonasscheid about 1 year ago - 4 comments

#279 - Ensure Percolator target decoy competition

Pull Request - State: closed - Opened by jonasscheid about 1 year ago - 1 comment

#278 - Class1 prediction folder is empty

Issue - State: open - Opened by jonasscheid about 1 year ago
Labels: bug

#277 - Add support for sdrf input

Issue - State: open - Opened by jonasscheid over 1 year ago
Labels: enhancement

#276 - MapRTTransformer does not change RT according to trafoXML

Issue - State: closed - Opened by jonasscheid over 1 year ago - 6 comments
Labels: bug

#275 - Fixed extra flag setting for ms2pip

Pull Request - State: closed - Opened by steffenlem over 1 year ago - 1 comment

#274 - Important! Template update for nf-core/tools v2.9

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 1 comment

#273 - Optimize resource allocations

Pull Request - State: closed - Opened by jonasscheid over 1 year ago - 1 comment

#272 - Dev

Pull Request - State: closed - Opened by steffenlem over 1 year ago - 1 comment

#271 - Add Filefilter after rawfile parsing

Pull Request - State: closed - Opened by jonasscheid over 1 year ago - 2 comments

#270 - Added MS2pip

Pull Request - State: closed - Opened by steffenlem over 1 year ago - 1 comment

#269 - Added Deeplc

Pull Request - State: closed - Opened by steffenlem over 1 year ago - 2 comments

#268 - fix rawfileparser output bug

Pull Request - State: closed - Opened by jonasscheid over 1 year ago - 1 comment

#267 - Add bruker file converter tdf2mzml

Pull Request - State: closed - Opened by jonasscheid over 1 year ago - 1 comment

#266 - Update openms version

Pull Request - State: closed - Opened by jonasscheid over 1 year ago - 1 comment

#265 - Update to new openMS version 3.0.0

Issue - State: closed - Opened by jonasscheid over 1 year ago
Labels: enhancement

#264 - Important! Template update for nf-core/tools v2.8

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 1 comment

#263 - Add support for bruker files

Issue - State: closed - Opened by jonasscheid over 1 year ago
Labels: enhancement

#262 - Add licenses to py files in bin

Pull Request - State: closed - Opened by jonasscheid over 1 year ago - 1 comment

#261 - Add low-resolution test data

Issue - State: closed - Opened by jonasscheid over 1 year ago
Labels: enhancement

#260 - Release 2.4.1

Pull Request - State: closed - Opened by jonasscheid over 1 year ago - 2 comments

#259 - Update test configs

Pull Request - State: closed - Opened by jonasscheid over 1 year ago - 2 comments

#258 - Adjust decoy strategy and fdr_level flag

Pull Request - State: closed - Opened by jonasscheid over 1 year ago - 3 comments

#257 - Resolve Pythonblack issues

Pull Request - State: closed - Opened by marissaDubbelaar over 1 year ago - 1 comment

#256 - Resolve black issues

Pull Request - State: closed - Opened by marissaDubbelaar over 1 year ago - 1 comment

#255 - DecoyDatabase uses tryptic configuration to generate decoys

Issue - State: closed - Opened by jonasscheid over 1 year ago
Labels: bug

#254 - Added low resolution settings to pipeline

Pull Request - State: closed - Opened by steffenlem over 1 year ago - 2 comments

#253 - Prepare for 2.4.1 (patch)

Pull Request - State: closed - Opened by marissaDubbelaar over 1 year ago - 2 comments

#252 - get old dev

Pull Request - State: closed - Opened by jonasscheid over 1 year ago - 1 comment

#251 - FATAL: container creation failed: mount error: while mounting: destination doesn't exist in container

Issue - State: closed - Opened by charmoniumQ almost 2 years ago - 4 comments
Labels: bug

#250 - Duplicate peptide identifications

Issue - State: closed - Opened by steffenlem almost 2 years ago - 6 comments
Labels: bug

#249 - Important! Template update for nf-core/tools v2.7.2

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago - 2 comments

#248 - Adding generated proteins to reference database is erroneous

Issue - State: open - Opened by jonasscheid almost 2 years ago - 3 comments
Labels: bug

#247 - Important! Template update for nf-core/tools v2.7.1

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago - 2 comments

#246 - Handling the case when no significant hit where found

Issue - State: closed - Opened by steffenlem almost 2 years ago
Labels: enhancement

#245 - Update Fred2 to epytope

Issue - State: open - Opened by marissaDubbelaar almost 2 years ago
Labels: enhancement, wontfix

#244 - Incorporate suggestions from PR

Pull Request - State: closed - Opened by marissaDubbelaar almost 2 years ago - 1 comment

#243 - Preparing for v2.4.0 - Maroon Gold Boxer

Pull Request - State: closed - Opened by marissaDubbelaar almost 2 years ago - 4 comments

#242 - Change text of the allele_sheet parameter

Pull Request - State: closed - Opened by marissaDubbelaar almost 2 years ago - 1 comment

#241 - Issue annotation of the HLA alleles in parameters

Issue - State: closed - Opened by marissaDubbelaar almost 2 years ago
Labels: bug

#240 - Include OpenMS FileInfo to check for valid mzML files

Issue - State: closed - Opened by jonasscheid almost 2 years ago - 3 comments
Labels: enhancement

#239 - make ion annotator feature default false

Pull Request - State: closed - Opened by jonasscheid almost 2 years ago - 1 comment

#238 - Inclusion of a working ion annotator

Pull Request - State: closed - Opened by marissaDubbelaar about 2 years ago - 1 comment

#237 - Dev

Pull Request - State: closed - Opened by marissaDubbelaar about 2 years ago - 1 comment

#236 - Issue ion annotator feature

Issue - State: closed - Opened by marissaDubbelaar about 2 years ago
Labels: bug

#235 - Make ion annotation optional

Issue - State: closed - Opened by jonasscheid about 2 years ago
Labels: enhancement

#234 - Issue in the alignment step

Pull Request - State: closed - Opened by marissaDubbelaar about 2 years ago - 1 comment

#233 - Profile test and test_full cannot access ref database

Issue - State: closed - Opened by jonasscheid about 2 years ago - 4 comments
Labels: bug

#232 - Increment changelog and docs

Pull Request - State: closed - Opened by jonasscheid about 2 years ago - 1 comment

#231 - Process labeled data

Issue - State: closed - Opened by jonasscheid about 2 years ago - 1 comment
Labels: enhancement

#230 - Issue in the MzTabExporter

Issue - State: closed - Opened by marissaDubbelaar about 2 years ago - 4 comments
Labels: bug

#229 - Add ion annotation feature

Pull Request - State: closed - Opened by jonasscheid about 2 years ago - 2 comments

#228 - Inconsistent annotation fdr_level parameters

Issue - State: closed - Opened by marissaDubbelaar about 2 years ago
Labels: enhancement

#227 - Nf core template merge 2.5.1

Pull Request - State: closed - Opened by marissaDubbelaar about 2 years ago - 1 comment

#226 - Important! Template update for nf-core/tools v2.6

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago - 2 comments

#225 - Comet: theoretical_fragment_ion parameter missing

Issue - State: closed - Opened by jonasscheid about 2 years ago - 1 comment
Labels: enhancement

#224 - Important! Template update for nf-core/tools v2.5.1

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago - 1 comment

#223 - Important! Template update for nf-core/tools v2.5

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago - 2 comments

#222 - Update openMS, renaming (sub)processes and inclusion of cometAdapter output

Pull Request - State: closed - Opened by marissaDubbelaar about 2 years ago - 2 comments

#221 - Refactor check samplesheet

Pull Request - State: closed - Opened by marissaDubbelaar over 2 years ago - 1 comment

#220 - Ion identification within a mass spectrum

Issue - State: closed - Opened by polklin over 2 years ago - 2 comments
Labels: enhancement

#219 - Important! Template update for nf-core/tools v2.4

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago - 1 comment

#218 - Update CHANGELOG.md

Pull Request - State: closed - Opened by jonasscheid over 2 years ago - 1 comment

#217 - Prepare for release 2.3.1

Pull Request - State: closed - Opened by marissaDubbelaar over 2 years ago - 2 comments

#216 - Inclusion of $mods in command

Pull Request - State: closed - Opened by marissaDubbelaar over 2 years ago - 1 comment

#215 - Resolve fixed modifications issue

Pull Request - State: closed - Opened by marissaDubbelaar over 2 years ago - 2 comments

#214 - Prepare for release 2.3.1

Pull Request - State: closed - Opened by marissaDubbelaar over 2 years ago - 2 comments

#213 - include a fix for issue #212

Pull Request - State: closed - Opened by marissaDubbelaar over 2 years ago - 1 comment

#212 - problem --fixed_modification

Issue - State: closed - Opened by marissaDubbelaar over 2 years ago
Labels: bug

#211 - Missing mzTab files

Issue - State: closed - Opened by marissaDubbelaar over 2 years ago
Labels: bug

#210 - Update nextflow_schema.json and fix mzTab output

Pull Request - State: closed - Opened by marissaDubbelaar over 2 years ago - 1 comment

#209 - Supporting alteration for the template and PR suggestions

Pull Request - State: closed - Opened by marissaDubbelaar over 2 years ago - 1 comment

#208 - Prepare for release 2.3.0

Pull Request - State: closed - Opened by marissaDubbelaar over 2 years ago - 1 comment

#207 - Pipeline summary

Pull Request - State: closed - Opened by marissaDubbelaar over 2 years ago - 1 comment

#206 - Updated workflow picture in nf-core design

Pull Request - State: closed - Opened by SusiJo over 2 years ago - 1 comment

#205 - Update readme

Pull Request - State: closed - Opened by marissaDubbelaar over 2 years ago - 1 comment

#204 - Important! Template update for nf-core/tools v2.3.2

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago - 1 comment

GitHub / nf-core/mhcquant issues and pull requests